ESSENTIAL CELL BIOLOGY CHAPTER
#4 - PROTEIN STRUCTURE & FUNCTION
EXAM QUESTIONS WITH VERIFIED
ANSWERS
Prions - ANSWER-Misfolded proteins that form aggregates that can damage to cells
and whole tissues.
It is infectious and causes neurodegenerative diseases like Alzheimer's or mad cow
disease.
Question 4-1: Urea is a molecule that
disrupts the hydrogen-bonded
network of water molecules. Why
might high concentrations of urea
unfold proteins? The structure of
urea is shown here. - ANSWER-Urea is a very small molecule that functions both as an
efficient hydrogen-bond donor (through its -NH2 groups) and as an efficient Hydrogen
bond acceptor (through its -c=o group). It can squeeze between hydrogen bonds that
stabilize protein molecules and thus destabilize protein structures.
In addition, nonpolar side chains are held together in the interior of folded proteins
because they disrupt the structure of water if they are exposed.
At high concentrations of urea, the H-bonded network of water molecules becomes
disrupted so that these hydrophobic forces are significantly diminished.
Proteins unfold in urea as a consequence of its effect on these two forces.
Chaperone proteins - ANSWER-Assists proteins to fold into its correct conformation
What can other chaperone proteins act as to help a polypeptide fold? - ANSWER-
Isolation chamber
What kind of shapes can proteins have? - ANSWER-Globular or fibrous
(Proteins can form filaments, sheets, rings, spheres)
α-helix - ANSWER-A spiral folding pattern
A hydrogen bond is between every 4th amino acid, this links the carboxylic group from
one bond to the amino group of another
, All the side chains are hydrophobic and point INWARD
Secondary structure
β-sheets - ANSWER-Made when hydrogen bonds forms between segments of
polypeptide chains lying side by side
Consists of 3 sheets
When neighboring polypeptide chains run in the same directions = Parallel
When neighboring polypeptide chains run in opposite directions (up & down) =
antiparallel
Anti parallel & parallel β-sheets both form rigid pleated structures
β-sheets can have a hydrophilic (polar) and a hydrophobic (non polar)
Secondary structure
Question 4-3: Remembering that the amino
acid side chains projecting from
each polypeptide backbone in a
β sheet point alternately above
and below the plane of the sheet, consider
the following protein sequence:
Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-
Leu-Lys-Ile-Arg-Phe-Glu.
Do you find anything remarkable about the
arrangement of the amino acids in
this sequence when incorporated
into a β sheet? Can you make any
predictions as to how the β sheet
might be arranged in a protein? - ANSWER-The amino acid sequence consists of
alternating nonpolar and charged or polar amino acids. The resulting strand in a beta
sheet would therefore be polar on one side and hydrophobic on the other. Such a strand
would probably be surrounded on either side by similar strands that together from a
beta sheet with a hydrophobic and polar face. In a protein, such a beta sheet would be
positioned so that the hydrophobic side would face the protein's interior and the polar
side would be on its surface, exposed to the water outside.
Proteins primary structure - ANSWER-Sequence of amino acids
#4 - PROTEIN STRUCTURE & FUNCTION
EXAM QUESTIONS WITH VERIFIED
ANSWERS
Prions - ANSWER-Misfolded proteins that form aggregates that can damage to cells
and whole tissues.
It is infectious and causes neurodegenerative diseases like Alzheimer's or mad cow
disease.
Question 4-1: Urea is a molecule that
disrupts the hydrogen-bonded
network of water molecules. Why
might high concentrations of urea
unfold proteins? The structure of
urea is shown here. - ANSWER-Urea is a very small molecule that functions both as an
efficient hydrogen-bond donor (through its -NH2 groups) and as an efficient Hydrogen
bond acceptor (through its -c=o group). It can squeeze between hydrogen bonds that
stabilize protein molecules and thus destabilize protein structures.
In addition, nonpolar side chains are held together in the interior of folded proteins
because they disrupt the structure of water if they are exposed.
At high concentrations of urea, the H-bonded network of water molecules becomes
disrupted so that these hydrophobic forces are significantly diminished.
Proteins unfold in urea as a consequence of its effect on these two forces.
Chaperone proteins - ANSWER-Assists proteins to fold into its correct conformation
What can other chaperone proteins act as to help a polypeptide fold? - ANSWER-
Isolation chamber
What kind of shapes can proteins have? - ANSWER-Globular or fibrous
(Proteins can form filaments, sheets, rings, spheres)
α-helix - ANSWER-A spiral folding pattern
A hydrogen bond is between every 4th amino acid, this links the carboxylic group from
one bond to the amino group of another
, All the side chains are hydrophobic and point INWARD
Secondary structure
β-sheets - ANSWER-Made when hydrogen bonds forms between segments of
polypeptide chains lying side by side
Consists of 3 sheets
When neighboring polypeptide chains run in the same directions = Parallel
When neighboring polypeptide chains run in opposite directions (up & down) =
antiparallel
Anti parallel & parallel β-sheets both form rigid pleated structures
β-sheets can have a hydrophilic (polar) and a hydrophobic (non polar)
Secondary structure
Question 4-3: Remembering that the amino
acid side chains projecting from
each polypeptide backbone in a
β sheet point alternately above
and below the plane of the sheet, consider
the following protein sequence:
Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-
Leu-Lys-Ile-Arg-Phe-Glu.
Do you find anything remarkable about the
arrangement of the amino acids in
this sequence when incorporated
into a β sheet? Can you make any
predictions as to how the β sheet
might be arranged in a protein? - ANSWER-The amino acid sequence consists of
alternating nonpolar and charged or polar amino acids. The resulting strand in a beta
sheet would therefore be polar on one side and hydrophobic on the other. Such a strand
would probably be surrounded on either side by similar strands that together from a
beta sheet with a hydrophobic and polar face. In a protein, such a beta sheet would be
positioned so that the hydrophobic side would face the protein's interior and the polar
side would be on its surface, exposed to the water outside.
Proteins primary structure - ANSWER-Sequence of amino acids
